Fluorescent pteridine-based nucleoside analogs that can be site-specifically incorporated into DNA oligonucleotides through a phosphodiester linkage have been developed and patented. The fluorescence properties of a series of these compounds have been characterized and potential applications are being investigated. These new fluorophores are promising probes for the study of protein/DNA interactions, because they are not attached to DNA externally and they do not appear to disrupt the tertiary structure of DNA. Rapid fluorescence-based assays for HIV-1 integrase and alkylguanine-DNA-akyltransferase have been developed, and the utility of these fluorophores as hybridization probes has been patented and is under investigation. A number of collaborative studies investigating the potential applications of these new research tools are also underway, and the probes have been licensed by Trilink Technologies and are commercially available.